update author list in license for (JAL-826)

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index dc70c47..04977e8 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.datamodel;
 
@@ -44,6 +43,8 @@ public class Alignment implements AlignmentI
   public static final int PROTEIN = 0;
 
   public static final int NUCLEOTIDE = 1;
+  
+  public boolean hasRNAStructure = false;
 
   /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
@@ -144,7 +145,7 @@ public class Alignment implements AlignmentI
    */
   public SequenceI getSequenceAt(int i)
   {
-    if (i < sequences.size())
+    if (i>-1 && i < sequences.size())
     {
       return (SequenceI) sequences.elementAt(i);
     }
@@ -345,11 +346,13 @@ public class Alignment implements AlignmentI
 
   /**
    * remove any annotation that references gp
-   * @param gp (if null, removes all group associated annotation)
+   * 
+   * @param gp
+   *          (if null, removes all group associated annotation)
    */
   private void removeAnnotationForGroup(SequenceGroup gp)
   {
-    if (annotations==null || annotations.length==0)
+    if (annotations == null || annotations.length == 0)
     {
       return;
     }
@@ -592,8 +595,8 @@ public class Alignment implements AlignmentI
     for (int i = 0; i < sequences.size(); i++)
     {
       Sequence seq = (Sequence) sequences.elementAt(i);
-      seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
-              '-', gc).replace(' ', gc));
+      seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+              .replace('-', gc).replace(' ', gc));
     }
   }
 
@@ -607,20 +610,36 @@ public class Alignment implements AlignmentI
     return gapCharacter;
   }
 
-  /**
-   * DOCUMENT ME!
+  /*
+   * (non-Javadoc)
    * 
-   * @return DOCUMENT ME!
+   * @see jalview.datamodel.AlignmentI#isAligned()
    */
   public boolean isAligned()
   {
-    int width = getWidth();
+    return isAligned(false);
+  }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+   */
+  public boolean isAligned(boolean includeHidden)
+  {
+    int width = getWidth();
+    if (hiddenSequences == null || hiddenSequences.getSize() == 0)
+    {
+      includeHidden = true; // no hidden sequences to check against.
+    }
     for (int i = 0; i < sequences.size(); i++)
     {
-      if (getSequenceAt(i).getLength() != width)
+      if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
       {
-        return false;
+        if (getSequenceAt(i).getLength() != width)
+        {
+          return false;
+        }
       }
     }
 
@@ -635,6 +654,11 @@ public class Alignment implements AlignmentI
    */
   public boolean deleteAnnotation(AlignmentAnnotation aa)
   {
+    return deleteAnnotation(aa, true);
+  }
+  
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+  {
     int aSize = 1;
 
     if (annotations != null)
@@ -666,7 +690,9 @@ public class Alignment implements AlignmentI
     if (swap)
     {
       annotations = temp;
-      unhookAnnotation(aa);
+      if (unhook) {
+        unhookAnnotation(aa);
+      }
     }
     return swap;
   }
@@ -708,6 +734,10 @@ public class Alignment implements AlignmentI
    */
   public void addAnnotation(AlignmentAnnotation aa, int pos)
   {
+    if(aa.getRNAStruc()!= null){
+      hasRNAStructure=true;
+    }
+    
     int aSize = 1;
     if (annotations != null)
     {
@@ -808,6 +838,11 @@ public class Alignment implements AlignmentI
       return false;
     }
   }
+  
+  public boolean hasRNAStructure(){
+    //TODO can it happen that structure is removed from alignment?
+    return hasRNAStructure;
+  }
 
   public void setDataset(Alignment data)
   {